My computer is a .pdf’ing mess!

February 7, 2008 11:17 AM

Help! My laptop is a nightmare of unorganized .pdfs, and if I have to create any more staggered files I might just lose my mind. Is there a program specifically designed to help me manage this deluge of information?

I am currently undertaking an independent research study (under the guidance of a faculty advisor), and actively working on amassing substantive secondary sources that I plan to cite in the composition of my thesis.

As a student of religious studies, I must rely on scholarly journals and academic articles to a large degree. As such, I find myself literally drowning in pdfs. So much so that I recently had no recourse but to purchase an external hard-drive just to free up enough room on my MacBook to run regular programs like Word and Keynote, etc.

After reading this post, I realized that there must be a better way of organizing my research. There must be, right?

What program can I use to organize my .pdf collection? I would like a program that is downloadable and computer-based (and not web-based, as our internet connection is sometimes spotty late at night, during which I do the majority of my research). I’m not a scientist in the traditional sense of the word, so I am unsure how helpful the suggested programs here or here would be to me. Is there a program specially suited to scholars in the humanities?

So, my criteria is:

• Downloadable, computer-based application for organizing pdfs
• Compatible with a MacBook running Mac OSX 10.5.1 (Leopard)
• Automatic attribution of Title and Author to the file name
• Will allow me to automatically save to the program folder (instead of to the desktop)
• Someone to hold my hand and painstakingly spell out the pros and cons of each program, as I am a lamebrain when it comes to most things technology-based.
• If the program is as intuitive as most mac programs appear to be, all the better!

HOPE ME, HIVEMIND!

BONUS: If you solve this quandary for me, I will gladly do one of the following: (a) draw a picture for you; (b) create an analog mock-up of your use page akin to this); or (c) send you a valentine!

posted by numinous to computers & internet (31 comments total)

I've been using Zotero for a few weeks now and it has completely streamlined the way I collect sources and citations. If you don't mind being locked into Firefox for cataloging your PDFs then go for it. Their introduction video gives a good idea of what type plug in can do.
posted by wfrgms at 11:24 AM on February 7, 2008

You're looking for Yep, or possibly its sibling Leap.
posted by unSane at 11:34 AM on February 7, 2008

Well, there's Papers. It seems specifically designed to manage academic articles, looks extremely well-done, and even won an Apple Design Award. That said, I've got no personal experience with it -- I'm not an acedemic -- so I can't give a personally recommendation. I think, though, it's probably what you're looking for.

I know a number of people who swear by DevonThink (a sort of personal database for digital detritus). It seems very oriented to folks with massive collections, and has all sorts of PDF-centric features including fast full text searching.

Personally I use Yojimbo to manage my digital ephemera, which, though extremely clean and simple, doesn't seem oriented around the hundreds of PDFs you're complaining of.
posted by jacobian at 11:36 AM on February 7, 2008

Seconding Zotero. It's truly incredible, and its facilities for automatically downloading citation info are nothing short of awe-inspiring.
posted by nasreddin at 11:37 AM on February 7, 2008

Oh yeah, this AskMe may be of use to you - it's where I first saw Zotero recommended.
posted by wfrgms at 11:41 AM on February 7, 2008

You can use iTunes manage PDFs and files will have the same metadata available to you that you'd have for music or video. Of course, authors would be listed as artists. You could use audio-only fields like BPM for something more relevant. Of course, you'd customize Genre to be more appropriate. You'd probably want to set up a separate library for the PDFs to keep your music separate from your documents. Instead of saving the libary in the music folder, you could keep it in documents, etc.

iTunes search won't look for text inside the PDFs in queries, but you can use Spotlight for that.
posted by birdherder at 11:43 AM on February 7, 2008

wfrgms - I've seen Zotero before, but occasionally I need to be able to access my collection of pdfs when I don't have access to a wireless signal, so unfortunately (and SO unfortunately, because Zotero looks fantastic), it's a no-go.

unSane - Briefly looking at both of these programs, they appear to be very close to what I'm after! However, this confuses me: "Yep leaves them all in place so organize them on disk however you want." Does this mean that if I download a pdf file, it will still download to my desktop, thus forcing me to drag it into a file to organize it? That might be a deal-breaker for me. The leap looks promising as something I would use in addition to what I'm currently looking for. I will definitely consider these as viable options, though.
posted by numinous at 11:47 AM on February 7, 2008

birdherder - you just completely blew my mind. I don't even know where to start (or even how to start) organizing my pdfs via iTunes. The idea of that scares me, as I like to compartmentalize my use of technology into user-friendly, distinct categories. I think this would confuse me more than anything! (Have I mentioned yet that I am a complete luddite?)
posted by numinous at 11:51 AM on February 7, 2008

Ignore-me-if-I'm-hijacking-but-I-hope-I'm-Not filter:

Yojimbo and Devonthink look like just the thing for our Mac. Are there analogous organizers for the PC?
posted by JimN2TAW at 11:56 AM on February 7, 2008 [2 favorites]

I need to be able to access my collection of pdfs when I don't have access to a wireless signal, so unfortunately (and SO unfortunately, because Zotero looks fantastic), it's a no-go.

Zotero works great offline (it stores all of your snapshots and pdfs locally.) No internet needed.
posted by wfrgms at 11:57 AM on February 7, 2008

I'm an academic, recently purchased a MacBook, and I'm totally in love with Papers--it will organize citations and files and allow you to read and search for more articles all within the same program. One feature you will really like is that you can tell it where your PDFs are and it will import them into itself and then organize them all into folders by year and author. Very nice.
posted by hydropsyche at 11:59 AM on February 7, 2008

jacobian - Papers looks like a very promising program, and I really like the ability to take notes and save them to the file itself (goodbye post-it notes!). However, the fact that it's designed for the organization of scientific articles (which I assume is a more narrow definition of "scientific," given it's integration with the PubMed database) gives me pause. Also, I cannot tell whether or not Papers allows you to add tags to the articles to facilitate searching. Do you know if it offers this?
posted by numinous at 11:59 AM on February 7, 2008

I use Bookends for this purpose. This past week I rounded up all the random stray PDF files in my computer to one folder and have been linking them to Bookends reference entries, if I already had one, and making entries if I didn't. Bookends also renames files by author year.

It's comparable in cost to Papers, so it might be worth it to download and play around with both.
posted by needled at 12:04 PM on February 7, 2008

Yep is amazing, I use it to keep track of everything.
posted by bradbane at 12:08 PM on February 7, 2008

> Also, I cannot tell whether or not Papers allows you to add tags to the articles to facilitate searching. Do you know if it offers this?

Looks like it does, I think. There's a free demo to download, so you might want to give that a shot.
posted by jacobian at 12:16 PM on February 7, 2008

Another question about Zotero - so, I understand that it stores all the pdfs locally, but does that mean that I cannot alter the notes I've added to the pdf file unless I have internet access via the browser? I would need to have the ability to do this to my pdf files whether or not I have access to the internet.

Also, how do I add the pdfs that I already have downloaded on my computer to my newly minted Zotero "library," as it were?
posted by numinous at 12:19 PM on February 7, 2008

I use Papers (mentioned above), and it is excellent. It is designed to do what you want, and can now use Google Books or Google Scholar for searching. (Previous versions were only really useful to biologists). About 60% of the time it can automatically assign author and title information to the article; other times it needs a little help (ie. you do a Google Scholar search and pick which result is the correct one to match your pdf).
Similar programs are Yep (also above), and iPapers, which I have less experience with, but both seem good.
I would choose Papers, because it works with Google and is really easy to use. It is worth considering Yep, which allows you to assign tags to each PDF file. If you want to organise and search for things with tags, go for Yep, but if you're OK with organising and finding things with author names and titles, then papers is I think the better choice. iPapers has the advantage of being free, but does not search as well or provide tags. Where iPapers is outstanding is that it manages the supplemental data files that accompany most modern scientific articles. If this is not an issue for you, go with Papers.
posted by nowonmai at 12:23 PM on February 7, 2008

I maintain a huge library of PDFs on my Mac for general reading and I don't like being locked to a single program to manage them. For tagging, I use Punakea. It allows you to add keywords that are searchable by Spotlight and Quicksilver. It's a great way to add tags independent of any programs. And it's not limited to tagging PDFs - it allows tagging for any type of file. The program also includes a nice small app for browsing and organizing your tags and files. Best of all it's free.
posted by junesix at 12:32 PM on February 7, 2008

nowonmai, thank you for your detailed description. You mention that Papers works well with Google Books and Google Scholar, but does it integrate well with JStor/LexisNexis/etc? I use these types of databases most frequently.
posted by numinous at 12:33 PM on February 7, 2008

numinous, I suggest meeting with an academic librarian as soon as possible. Most academic libraries provide instruction in the form of workshops and web pages on software such as Zotero, EndNote, and Refworks. For example, the University of Michigan Library offers this citation management guide.

The reason I am mentioning citation management software is that you don't want to just organize and annotate the PDF files, you will be citing from them in your thesis and producing a bibliography. Modern reference management software will organize your PDFs, let you use tags or keywords for easy finding, AND allow you to export the citation info in the citation format of your choice.

If compatibility and easy connection with your university library catalog is an issue, EndNote is probably your best bet. It's probably the most widely used citation management software. What this means is that if you encounter any problems or questions somebody else may already have answered that. Your university library will be able to help out. You can exchange EndNote files with colleagues. And so on.

I myself dislike EndNote because of my experience with previous OS X versions, although I hear the latest version isn't bad, and have been using Bookends, like I stated above. On the other hand, I am perfectly willing to read the manual and support forums and devise workarounds and tweak things to my liking. Bookends is very easy and straightforward to use, I think, but I've had colleagues switch back to EndNotes because of compatibility issues with their colleagues.
posted by needled at 12:38 PM on February 7, 2008

re: JStor/Lexis Nexis etc: the answer is "not yet". The guys who make Papers are biologists, but they encourage other people to write plugins for other repositories. As of today, there are not very many and the only ones that would be useful in your field would be Google Books and Google Scholar. They also have Web of Science, which includes a lot of social sciences, if that's any help?
I think you should be able to dump your PDFs into Papers and use Google to assign authors and titles to the academic articles, but Lexis Nexis is far beyond my ken so I can't really advise. Perhaps try using Google Scholar for a few searches to see if it is adequate for your needs?
posted by nowonmai at 12:49 PM on February 7, 2008

numinous, everything Zotero does is locally stored in your Firefox profile directory, and you can tell it to keep all your PDFs in there too. You can change notes, add bibliography, whatever, and it's all just an offline MySQL database.
posted by nasreddin at 12:49 PM on February 7, 2008

Directly exporting JSTOR citations.
posted by needled at 12:51 PM on February 7, 2008

In addition to organizing PDFs, Papers works as a citation management guide, including for things you might not have a PDF of, but it does not integrate with Microsoft Word. However, it is very easy to assemble your citations and export them to EndNote (or something else which your university may provide for free) which does integrate with Word.

Papers works with JSTOR seamlessly. I have not tried it with LexisNexis, but assuming it can be accessed in a web browser I think it will work with any database.

Also, while Papers doesn't have a space for tags in particular, it uses Spotlight to search the entire citation for an article, so if you added tags to one of the other boxes it would find them.
posted by hydropsyche at 12:52 PM on February 7, 2008

needled, thanks for the heads up about the citation management software (this will prove to be very, very helpful in the weeks to come). I asked the online library consultant (via the University's new! interactive! chat service!), and they pointed me to some workshops on EndNote. I have signed up for one, and will report back in a few weeks as to whether this was helpful.

nasreddin - you say 'MySQL,' and I say 'whuh??' Honestly, I don't even know what that means. :(

hydropsyche - If Papers works as well with JStor as you say it does, I am very hopeful about it. Perhaps I can make up for the lack of tags with Punakea that junesix links to?

I know this sounds ridiculous to those of you who are polyglot in various computer languages, but the sheer amount of technology in this thread is totally overwhelming to me.
posted by numinous at 1:12 PM on February 7, 2008

I use bibdesk to organize my PDFs. Don't be put off by the bibtex stuff, you don't even have to use that part of the program if you don't want to. (Also, with a little bit of work, it is possible to configure it to produce citations that you could paste into word or whatever, not just LaTeX.)
posted by advil at 1:21 PM on February 7, 2008

There have been so many great suggestions - ones better than this one - but for a broader range of files, I accomplish what you're looking for with Adobe Bridge.

I also have to give a shout-out to Issuu, which is a web-based way to stylishly and effectively read & upload PDF files to blogs and other sites. I love it - it makes reading my PDF collection a little easier, especially when I can easily upload a few to my blog and then read them on the road on any internet connection.
posted by Detuned Radio at 1:22 PM on February 7, 2008

Zotero is your solution. Works perfectly offline, online tool for collaboration in the works. Papers looks interesting, but €29 for something implemented just as well or better, with superior community support in zotero ... can't see the value that paying money is bringing me, thanks.
posted by singingfish at 1:51 PM on February 7, 2008

Numinous - Zotero never needs to be online at a point where you aren't already online, i. e. getting the original pdf. Everything about Zotero is offline except that first time you tell it to capture the article. It has its own offline database (the "MySQL" part) that stores all your notes, tags, and bibliographical information and it captures a snapshot of the page as well as downloading a copy of the pdf if there is one available.

The only non-obvious thing about Zotero I've noticed so far is that you have to go into its options page and manually tell it to get the pdf indexer (at which point I noticed it starting to download pdfs). Zotero only has one fault -- that it doesn't yet work with Firefox 3.
posted by The Bishop of Turkey at 1:54 PM on February 7, 2008

You may find the information on this page helpful, it seems to focus on the academic software needs of humanities scholars.
posted by needled at 10:54 AM on February 8, 2008

Papers, the software discussed above, has a new version which now searches additional databases including JStor (but not Lexis Nexis).
posted by nowonmai at 1:14 PM on May 13, 2008